"Neko Neko Fantasia" centers on a fantastical world where humans and anthropomorphic cat-like beings, known as Nekos, coexist. The narrative unfolds in the kingdom of Felinia, a land where magic and technology are intertwined. The protagonist, a young human named Kaito, discovers he possesses a rare ability to communicate with Nekos, a skill thought to be lost for centuries. This ability draws him into a conflict between the Nekos and a shadowy organization seeking to exploit their magical powers for nefarious purposes.

Kaito is joined by a group of Neko companions, each with unique abilities and personalities. Among them is Miko, a skilled warrior with a mysterious past; Tora, a mischievous but loyal inventor; and Shiro, a wise and reserved mage. Together, they embark on a journey to uncover the truth behind the organization's plans and protect the balance between humans and Nekos. Along the way, they encounter various challenges, including ancient ruins, magical artifacts, and rival factions vying for control of Felinia's resources.

The plot delves into themes of coexistence, trust, and the consequences of power. As Kaito and his companions uncover the organization's true motives, they must confront their own beliefs and the complexities of their world. The story balances action, mystery, and character development, with a focus on the evolving relationships between the human and Neko characters. The narrative builds toward a climactic confrontation that tests their resolve and the bonds they have formed, ultimately shaping the future of Felinia.